Tests of selection

1. Tests of diversity

2. Tests of tree shape

3. Tests of evolutionary rates

Test: is there less genetic diversity than expected?

Influenza phylogeny and effective number of infections

Coalescent rates in flu and measles

Selective sweeps purge diversity

Test: is the tree shape different from the neutral expectation?

Tajima's D statistic summarizes deviation from neutrality

Influenza has negative Tajima's D

Test: is there an overabundance of fixed non-synonymous mutations?

"Trunk" branches show an excess of non-synonymous change at epitope sites in influenza

Abundance of green epitope mutations on phylogeny trunk, relative to blue synonymous and red non-epitope mutations

Can be extended to look at relationship between mutations and clade growth